In Magento 2 - How to remove a column in customer_entity table?

In your setup script, we can use dropColumn:

 $setup->getConnection()->dropColumn($setup->getTable('your_table'), 'your_column');

You can try this simple dropColumn() function in your installer script.

$this->startSetup();

//example: 
$this->getConnection()->dropColumn($this->getTable('your_table_definition'), 'your column name', $schemaName = null)

$this->endSetup();

Here is my solution, maybe good for referring for other.
I created Tohq\Customer\Setup\UpgradeSchema.php file:

<?php

namespace Tohq\Customer\Setup;

use Magento\Framework\Setup\UpgradeSchemaInterface;
use Magento\Framework\Setup\ModuleContextInterface;
use Magento\Framework\Setup\SchemaSetupInterface;

/**
 * @codeCoverageIgnore
 */
class UpgradeSchema implements UpgradeSchemaInterface
{
    public function upgrade(SchemaSetupInterface $setup, ModuleContextInterface $context)
    {            
        // Version of module in setup table is less then the give value.
        if (version_compare($context->getVersion(), '0.1.4', '<')) {

            // get table customer_entity
            $eavTable = $setup->getTable('customer_entity');

            // Check if the table already exists
            if ($setup->getConnection()->isTableExists($eavTable) == true) {
                $connection = $setup->getConnection();

                // del_flg = column name which you want to delete
                $connection->dropColumn($eavTable, 'del_flg');
            }
        }

    }
}